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Prokaryotic type KH domain (KH-domain type II) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Alpha-lytic protease prodomain-like [ 54805] (10)
Superfamily:   Prokaryotic type KH domain (KH-domain type II) [ 54814]
Families:   Prokaryotic type KH domain (KH-domain type II) [ 54815] (4)


Superfamily statistics
Genomes (3,250) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,324 80,143 20
Proteins 10,646 64,089 16


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular component organization or biogenesis 0.0006427 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.003818 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.04722 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02395 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.8318 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.3668 Least Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.00000001427 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000007658 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00003889 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0.000128 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0001797 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.0009966 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.04218 Moderately Informative Inherited
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Informative Direct
Biological Process (BP) organelle assembly 0.000000000001057 Informative Direct
Biological Process (BP) ribosome assembly 0.0000000002211 Highly Informative Direct
Molecular Function (MF) binding 0.02701 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.0000000004092 Moderately Informative Direct
Molecular Function (MF) anion binding 0.02034 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.03422 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.009238 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.3634 Moderately Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.00000002631 Informative Direct
Molecular Function (MF) RNA binding 0.000007074 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0001757 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.0003744 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.000425 Informative Direct
Molecular Function (MF) purine nucleoside binding 0.0000007043 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00007147 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3826 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.03356 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.07353 Least Informative Inherited
Cellular Component (CC) ribosome 0.000002773 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.000003455 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.07574 Moderately Informative Inherited
Cellular Component (CC) small ribosomal subunit 0.0000000000005607 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.00000000004651 Informative Direct
Cellular Component (CC) cytosolic small ribosomal subunit 0.000000000000003036 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation1Moderately InformativeInherited
Biological processRibosome biogenesis0InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentMembrane0.000000000001784Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell inner membrane0.000000002825InformativeDirect
Molecular functionNucleotide-binding0.1012Least InformativeInherited
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009019 SSF54814 Protein matches
Abstract

The K homology domain is a common RNA-binding motif present in one or multiple copies in both prokaryotic and eukaryotic regulatory proteins. The KH motifs may act cooperatively to bind RNA in the case of multiple motifs, or independently in the case of single KH motif proteins. Prokaryotic (pKH) and eukaryotic (eKH) KH domains share a KH-motif, but have different topologies. The pKH domain has been found in a number of proteins, including the N-terminal domain of the S3 ribosomal protein [PubMed11014182], the C-terminal domain of Era GTPase [PubMed10411886] and the two C-terminal domains of the NusA transcription factor [PubMed11430821]. The structure of the pKH domain consists of a two-layer alpha/beta fold in the arrangement alpha/beta(2)/alpha/beta.

More information about these proteins can be found at Protein of the Month: RNA Exosomes.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 10 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Prokaryotic type KH domain (KH-domain type II) domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 10 hidden Markov models representing the Prokaryotic type KH domain (KH-domain type II) superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]